[ccp4bb] SHELXL/ BAVERAGE
Dear all: I am dealing with a SHELXL/ BAVERAGE issue. I have refined a few structures in SHELXL but I think I am not converting properly the coordinates into the .pdb format. I am trying to use Baverage but I get an error The program run with command: baverage XYZIN C:/datasets/34_MolP.pdb XYZOUT C:/datasets/34_MolP_baverage1.pdb RMSTAB C:/datasets/34_MolP_bavrmstab1.txt has failed with error message BAVERAGE: XYZOPEN: Error opening logical name XYZIN Thank you very much. Any comments will be appreciated. Fátima
Re: [ccp4bb] Density peaks to build
Dear Chris and Leo, Thank you for your suggestions. I am refining the 1.08 A structure in SHELXL and I have Hs added; I think refinement is at a final stage. I did start with the 50%, 25+25% occupancy but then I changed to 0.33 each ... I need to refine this further. For the 1.35A data, model is complete (except for some C- and N-terminal residues) and I've refined alternative conformations too. The crystallization condition is Sodium acetate and PEG3350 with ethylene glycol as cryo. I have some molecules of cryo and Na in the model. I’ll try other cat/anions and refine. Best, Fátima
[ccp4bb] Ligand weak density in SHELXL
Dear all, I solved the structure of an enzyme at resolution of 1.1A with a bound substrate using Refmac5 and Coot for refinement/building. I have a very nice density for my ligand and a very good structure, as judged by Molprobity analysis. Now I'm using SHELXL to finish refinement but most of the density for my ligand disappears when I put it in, and it gets very high B factors. I though it could be some problem with the occupancy so I did a set of runs with different occupancies ranging from 0.2 to 1 and I got the best R factors when using 0.4/0.5 for the occupancy. However, I still have most of the ligand outside electron density… In Coot I get no ligand with “Find ligand” even when I reduce the cluster sigma level to 0.8. What am I missing here? Just another question, how to reduce the acceptable fit fraction in Coot “Find ligand”? Thanks for any advice, Fátima
